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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudaaligner</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">Alignment</a></li>  </ul>
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<a href="#pub-methods">Public Member Functions</a> &#124;
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<div class="title">claragenomics::cudaaligner::Alignment Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudaaligner.html">CUDA Aligner package</a></div></div>  </div>
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<p><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> - Object encapsulating an alignment between 2 string.  
 <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="alignment_8hpp_source.html">alignment.hpp</a>&gt;</code></p>
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Public Member Functions</h2></td></tr>
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virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a6479df67f21d643782abfed873218ea8">~Alignment</a> ()=default</td></tr>
<tr class="memdesc:a6479df67f21d643782abfed873218ea8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
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virtual const std::string &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab29dceafccd3cb0a2e87023c5d48a780">get_query_sequence</a> () const =0</td></tr>
<tr class="memdesc:ab29dceafccd3cb0a2e87023c5d48a780"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns query sequence. <br /></td></tr>
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<tr class="memitem:a4a61cdee74c32930f49cb878fc17db57"><td class="memItemLeft" align="right" valign="top"><a id="a4a61cdee74c32930f49cb878fc17db57"></a>
virtual const std::string &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4a61cdee74c32930f49cb878fc17db57">get_target_sequence</a> () const =0</td></tr>
<tr class="memdesc:a4a61cdee74c32930f49cb878fc17db57"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns target sequence. <br /></td></tr>
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<tr class="memitem:aeb4a583f6fbc643c93170797ca45a876"><td class="memItemLeft" align="right" valign="top">virtual std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">convert_to_cigar</a> () const =0</td></tr>
<tr class="memdesc:aeb4a583f6fbc643c93170797ca45a876"><td class="mdescLeft">&#160;</td><td class="mdescRight">Converts an alignment to CIGAR format. The is a reduced implementation of the CIGAR standard supporting only M, I and D states.  <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#aeb4a583f6fbc643c93170797ca45a876">More...</a><br /></td></tr>
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<tr class="memitem:ab22457c02ac00ec205dcd5a75b253881"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">get_alignment_type</a> () const =0</td></tr>
<tr class="memdesc:ab22457c02ac00ec205dcd5a75b253881"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns type of alignment.  <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#ab22457c02ac00ec205dcd5a75b253881">More...</a><br /></td></tr>
<tr class="separator:ab22457c02ac00ec205dcd5a75b253881"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7665f284b7929998357c89461e444f78"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">get_status</a> () const =0</td></tr>
<tr class="memdesc:a7665f284b7929998357c89461e444f78"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return status of alignment.  <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a7665f284b7929998357c89461e444f78">More...</a><br /></td></tr>
<tr class="separator:a7665f284b7929998357c89461e444f78"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5139f26517193e077000dcddfbc15f70"><td class="memItemLeft" align="right" valign="top">virtual const std::vector&lt; <a class="el" href="group__cudaaligner.html#ga8ee40da066dcb49eb0516b6a763ec45d">AlignmentState</a> &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">get_alignment</a> () const =0</td></tr>
<tr class="memdesc:a5139f26517193e077000dcddfbc15f70"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the alignment between sequences.  <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a5139f26517193e077000dcddfbc15f70">More...</a><br /></td></tr>
<tr class="separator:a5139f26517193e077000dcddfbc15f70"><td class="memSeparator" colspan="2">&#160;</td></tr>
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virtual <a class="el" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">FormattedAlignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#a4be4bb544d593f3fd7624628f2bda29c">format_alignment</a> () const =0</td></tr>
<tr class="memdesc:a4be4bb544d593f3fd7624628f2bda29c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Print formatted alignment to stderr. <br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> - Object encapsulating an alignment between 2 string. </p>
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<a id="aeb4a583f6fbc643c93170797ca45a876"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aeb4a583f6fbc643c93170797ca45a876">&#9670;&nbsp;</a></span>convert_to_cigar()</h2>

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          <td class="memname">virtual std::string claragenomics::cudaaligner::Alignment::convert_to_cigar </td>
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          <td> const</td>
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<p>Converts an alignment to CIGAR format. The is a reduced implementation of the CIGAR standard supporting only M, I and D states. </p>
<dl class="section return"><dt>Returns</dt><dd>CIGAR string </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a5139f26517193e077000dcddfbc15f70">&#9670;&nbsp;</a></span>get_alignment()</h2>

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          <td class="memname">virtual const std::vector&lt;<a class="el" href="group__cudaaligner.html#ga8ee40da066dcb49eb0516b6a763ec45d">AlignmentState</a>&gt;&amp; claragenomics::cudaaligner::Alignment::get_alignment </td>
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<p>Get the alignment between sequences. </p>
<dl class="section return"><dt>Returns</dt><dd>Vector of AlignmentState encoding sequence of match, mistmatch and insertions in alignment. </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#ab22457c02ac00ec205dcd5a75b253881">&#9670;&nbsp;</a></span>get_alignment_type()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> claragenomics::cudaaligner::Alignment::get_alignment_type </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
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<p>Returns type of alignment. </p>
<dl class="section return"><dt>Returns</dt><dd>Type of alignment </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a7665f284b7929998357c89461e444f78">&#9670;&nbsp;</a></span>get_status()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> claragenomics::cudaaligner::Alignment::get_status </td>
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<p>Return status of alignment. </p>
<dl class="section return"><dt>Returns</dt><dd>Status of alignment </dd></dl>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li>cudaaligner/include/claragenomics/cudaaligner/<a class="el" href="alignment_8hpp_source.html">alignment.hpp</a></li>
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